Enhanced Tetrahedral Ordering of Water Molecules in Minor Grooves of DNA: Relative Role of DNA Rigidity, Nanoconfinement, and Surface Specific Interactions
Autor: | Biman Bagchi, Biman Jana, Subrata Pal |
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Rok vydání: | 2010 |
Předmět: |
Configuration entropy
Water DNA Molecular Dynamics Simulation Surfaces Coatings and Films Crystallography Molecular dynamics chemistry.chemical_compound Water dynamics Temperature and pressure chemistry Materials Chemistry Tetrahedron Nanotechnology Thermodynamics Molecule Physical and Theoretical Chemistry Minor groove |
Zdroj: | The Journal of Physical Chemistry B. 114:3633-3638 |
ISSN: | 1520-5207 1520-6106 |
DOI: | 10.1021/jp907513w |
Popis: | Confinement and surface specific interactions can induce structures otherwise unstable at that temperature and pressure. Here we study the groove specific water dynamics in the nucleic acid sequences, poly-AT and poly-GC, in long B-DNA duplex chains by large scale atomistic molecular dynamics simulations, accompanied by thermodynamic analysis. While water dynamics in the major groove remains insensitive to the sequence differences, exactly the opposite is true for the minor groove water. Much slower water dynamics observed in the minor grooves (especially in the AT minor) can be attributed to an enhanced tetrahedral ordering (t(h)) of water. The largest value oft(h)in the AT minor groove is related to the spine of hydration found in X-ray structure. The calculated configurational entropy (S(C)) of the water molecules is found to be correlated with the self-diffusion coefficient of water in different region via Adam-Gibbs relation D = A exp(-B/TS(C)), and also witht(h). |
Databáze: | OpenAIRE |
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